Merge branch 'release_22.05' into dev

client/src/components/History/Content/ContentItem.vue

@@ -84,7 +84,7 @@
             <DatasetDetails
                 v-if="expandDataset"
                 :dataset="item"
-                :show-highlight="isHistoryItem && isHistPanel"
+                :show-highlight="isHistoryItem"
                 @edit="onEdit"
                 @toggleHighlights="toggleHighlights" />
         </b-collapse>
@@ -119,8 +119,7 @@ export default {
         highlight: { type: String, default: null },
         id: { type: Number, required: true },
         isDataset: { type: Boolean, default: true },
-        isHistoryItem: { type: Boolean, default: true },
-        isHistPanel: { type: Boolean, default: false },
+        isHistoryItem: { type: Boolean, default: false },
         item: { type: Object, required: true },
         name: { type: String, required: true },
         selected: { type: Boolean, default: false },

client/src/components/History/Content/GenericElement.vue

@@ -6,7 +6,6 @@
             :name="item.element_identifier"
             :is-dataset="item.element_type == 'hda'"
             :expand-dataset="expandDataset"
-            :is-history-item="false"
             @update:expand-dataset="expandDataset = $event"
             @view-collection="viewCollection = !viewCollection" />
         <GenericItem v-if="viewCollection" :item-id="item.object.id" :item-src="item.object.history_content_type" />

client/src/components/History/Content/GenericItem.vue

@@ -3,6 +3,7 @@
         <loading-span v-if="loading" message="Loading dataset" />
         <div v-else>
             <ContentItem
+                is-history-item
                 :id="item.hid"
                 :item="item"
                 :name="item.name"
@@ -10,9 +11,9 @@
                 :is-dataset="item.history_content_type == 'dataset'"
                 @update:expand-dataset="expandDataset = $event"
                 @view-collection="viewCollection = !viewCollection"
-                @delete="onDelete"
-                @undelete="onUndelete"
-                @unhide="onUnhide" />
+                @delete="onDelete(item)"
+                @undelete="onUndelete(item)"
+                @unhide="onUnhide(item)" />
             <div v-if="viewCollection">
                 <div v-for="(collectionItem, collectionIndex) in item.elements" :key="collectionIndex">
                     <GenericElement :item="collectionItem" />

client/src/components/History/CurrentCollection/CollectionPanel.vue

@@ -28,7 +28,6 @@
                                     :name="item.element_identifier"
                                     :expand-dataset="isExpanded(item)"
                                     :is-dataset="item.element_type == 'hda'"
-                                    :is-history-item="false"
                                     @update:expand-dataset="setExpanded(item, $event)"
                                     @view-collection="onViewSubCollection" />
                             </template>

client/src/components/History/CurrentHistory/HistoryPanel.vue

@@ -100,12 +100,12 @@
                                 <template v-slot:item="{ item, currentOffset }">
                                     <ContentItem
                                         v-if="!invisible[item.hid]"
+                                        is-history-item
                                         :id="item.hid"
                                         :item="item"
                                         :name="item.name"
                                         :expand-dataset="isExpanded(item)"
                                         :is-dataset="isDataset(item)"
-                                        is-hist-panel
                                         :highlight="getHighlight(item)"
                                         :selected="isSelected(item)"
                                         :selectable="showSelection"

client/src/components/Tags/tagService.js

@@ -57,10 +57,11 @@ export class TagService {
         if (!tag.valid) {
             throw new Error("Invalid tag");
         }
-        const url = `${getAppRoot()}tag/add_tag_async?item_id=${id}&item_class=${itemClass}&context=${context}&new_tag=${
-            tag.text
-        }`;
-        const response = await axios.get(url);
+        const url = `${getAppRoot()}tag/add_tag_async`;
+        const config = {
+            params: { item_id: id, item_class: itemClass, context: context, new_tag: tag.text },
+        };
+        const response = await axios.get(url, config);
         if (response.status !== 200) {
             throw new Error(`Unable to save tag: ${tag}`);
         }
@@ -75,10 +76,9 @@ export class TagService {
     async delete(rawTag) {
         const { id, itemClass, context } = this;
         const tag = createTag(rawTag);
-        const url = `${getAppRoot()}tag/remove_tag_async?item_id=${id}&item_class=${itemClass}&context=${context}&tag_name=${
-            tag.text
-        }`;
-        const response = await axios.get(url);
+        const url = `${getAppRoot()}tag/remove_tag_async`;
+        const config = { params: { item_id: id, item_class: itemClass, context: context, tag_name: tag.text } };
+        const response = await axios.get(url, config);
         if (response.status !== 200) {
             throw new Error(`Unable to delete tag: ${tag}`);
         }
@@ -92,8 +92,9 @@ export class TagService {
      */
     async autocomplete(searchText) {
         const { id, itemClass } = this;
-        const url = `${getAppRoot()}tag/tag_autocomplete_data?item_id=${id}&item_class=${itemClass}&q=${searchText}`;
-        const response = await axios.get(url);
+        const url = `${getAppRoot()}tag/tag_autocomplete_data`;
+        const config = { params: { item_id: id, item_class: itemClass, q: searchText } };
+        const response = await axios.get(url, config);
         if (response.status !== 200) {
             throw new Error(`Unable to retrieve autocomplete tags for search string: ${searchText}`);
         }

client/src/components/Tags/tagService.test.js

@@ -2,9 +2,6 @@ import axios from "axios";
 import MockAdapter from "axios-mock-adapter";
 import { TagService } from "./tagService";
 import { createTag } from "./model";
-//import { interval } from "rxjs";
-//import { take, takeUntil } from "rxjs/operators";
-// test response
 import autocompleteResponse from "./testData/autocompleteResponse.txt";
 
 describe("Tags/tagService.js", () => {
@@ -15,6 +12,12 @@ describe("Tags/tagService.js", () => {
         context: "",
         debounceInterval: 50, // shorter value than default for unit tests
     };
+    const testLabel = "fo0bar123";
+    const expectedParams = {
+        item_id: 123,
+        item_class: "fooClass",
+        context: "",
+    };
 
     const svc = new TagService(svcParams);
     beforeEach(() => {
@@ -26,43 +29,43 @@ describe("Tags/tagService.js", () => {
     });
 
     describe("save", () => {
-        const testLabel = "fo0bar123";
         const testTag = createTag(testLabel);
 
-        const { id, itemClass, context } = svcParams;
-        const expectedSaveUrl = `/tag/add_tag_async?item_id=${id}&item_class=${itemClass}&context=${context}&new_tag=${testLabel}`;
+        const expectedSaveUrl = `/tag/add_tag_async`;
 
         it("should save a string tag", async () => {
             const savedTag = await svc.save(testLabel);
             expect(savedTag.text).toBe(testLabel);
             expect(axiosMock.history.get[0].url).toBe(expectedSaveUrl);
+            expect(axiosMock.history.get[0].params).toEqual({ ...expectedParams, new_tag: testLabel });
         });
 
         it("should save an object tag", async () => {
             const savedTag = await svc.save(testTag);
             expect(savedTag.text).toBe(testLabel);
             expect(axiosMock.history.get[0].url).toBe(expectedSaveUrl);
+            expect(axiosMock.history.get[0].params).toEqual({ ...expectedParams, new_tag: testLabel });
         });
 
         // TODO: test error conditions
     });
     describe("delete", () => {
-        const testLabel = "fo0bar123";
         const testTag = createTag(testLabel);
 
-        const { id, itemClass, context } = svcParams;
-        const expectedDeleteUrl = `/tag/remove_tag_async?item_id=${id}&item_class=${itemClass}&context=${context}&tag_name=${testLabel}`;
+        const expectedDeleteUrl = `/tag/remove_tag_async`;
 
         it("should delete a text tag", async () => {
             const result = await svc.delete(testTag);
             expect(result).toBeTruthy();
             expect(axiosMock.history.get[0].url).toBe(expectedDeleteUrl);
+            expect(axiosMock.history.get[0].params).toEqual({ ...expectedParams, tag_name: testLabel });
         });
 
         it("should delete an object tag", async () => {
             const result = await svc.delete(testTag);
             expect(result).toBeTruthy();
             expect(axiosMock.history.get[0].url).toBe(expectedDeleteUrl);
+            expect(axiosMock.history.get[0].params).toEqual({ ...expectedParams, tag_name: testLabel });
         });
 
         // TODO: test error conditions
@@ -70,8 +73,7 @@ describe("Tags/tagService.js", () => {
 
     describe("autocomplete", () => {
         const searchString = "foo";
-        const { id, itemClass } = svcParams;
-        const expectedSearchUrl = `/tag/tag_autocomplete_data?item_id=${id}&item_class=${itemClass}&q=${searchString}`;
+        const expectedSearchUrl = `/tag/tag_autocomplete_data`;
 
         const checkAutocompleteResult = (result) => {
             expect(result).toBeTruthy();
@@ -83,46 +85,14 @@ describe("Tags/tagService.js", () => {
 
         // straight ajax request, unused in practice, but it's easier to
         // test this call if we just expose it
+        const { ...searchParams } = expectedParams;
+        delete searchParams.context;
+
         it("ajax call should return tag objects", async () => {
             const result = await svc.autocomplete(searchString);
             expect(axiosMock.history.get[0].url).toBe(expectedSearchUrl);
+            expect(axiosMock.history.get[0].params).toEqual({ ...searchParams, q: searchString });
             checkAutocompleteResult(result);
         });
-
-        /*
-
-        // hit the search input with multiple entries, only one ajax call
-        // should result because of debouncing
-        it("should debounce autocomplete search inputs", (done) => {
-            // stub ajax request to return the success response if the
-            // searchString is the expected input
-
-            // take first emission, debouncing should guarantee the first
-            // emission is the last thing we sent, should be searchString
-            const timer$ = interval(100).pipe(take(1));
-            const option$ = svc.autocompleteOptions.pipe(takeUntil(timer$));
-
-            const nextHandler = jest.fn();
-
-            option$.subscribe({
-                next: nextHandler,
-                error: (err) => console.warn("error", err),
-                complete: () => {
-                    expect(nextHandler).toHaveBeenCalledTimes(1);
-                    expect(axiosMock.history.get.length).toBe(1);
-                    done();
-                },
-            });
-
-            // spam a bunch of key inputs followed by the correct input
-            const spamCount = 2 + Math.floor(Math.random() * 10);
-            for (let i = 0; i < spamCount; i++) {
-                const spamVal = new String(Math.random());
-                svc.autocompleteSearchText = spamVal;
-            }
-            svc.autocompleteSearchText = searchString;
-        });
-
-        */
     });
 });

client/src/components/Tour/Tour.vue

@@ -86,6 +86,9 @@ export default {
         isLast() {
             return this.currentIndex === this.steps.length - 1;
         },
+        hasBegun() {
+            return this.currentIndex >= 1;
+        },
     },
     beforeDestroy() {
         window.removeEventListener("keyup", this.handleKeyup);
@@ -105,12 +108,15 @@ export default {
             }
         },
         loginRequired(user) {
-            return this.requirements.indexOf("logged_in") >= 0 && user.isAnonymous;
+            return !this.hasBegun && this.requirements.indexOf("logged_in") >= 0 && user.isAnonymous;
         },
         adminRequired(user) {
-            return this.requirements.indexOf("admin") >= 0 && !user.is_admin;
+            return !this.hasBegun && this.requirements.indexOf("admin") >= 0 && !user.is_admin;
         },
         newHistoryRequired(history) {
+            if (this.hasBegun) {
+                return false;
+            }
             const hasNewNistoryRequirement = this.requirements.indexOf("new_history") >= 0;
             if (!hasNewNistoryRequirement) {
                 return false;

client/src/components/Tour/runTour.js

@@ -4,7 +4,7 @@ import { mountVueComponent } from "utils/mountVueComponent";
 import Tour from "./Tour";
 
 // delays and maximum number of attempts to wait for element
-const attempts = 100;
+const attempts = 200;
 const delay = 200;
 
 // return tour data

client/src/mvc/dataset/dataset-model.js

@@ -75,7 +75,7 @@ var DatasetAssociation = Backbone.Model.extend(BASE_MVC.LoggableMixin).extend(
                     display: `datasets/${id}/display/?preview=True`,
                     edit: `datasets/edit?dataset_id=${id}`,
                     download: `api/datasets/${id}/display${this._downloadQueryParameters()}`,
-                    report_error: `dataset/errors?id=${id}`,
+                    report_error: `datasets/error?dataset_id=${id}`,
                     rerun: `tool_runner/rerun?id=${id}`,
                     show_params: `datasets/${id}/details`,
                     visualization: "visualization",

lib/galaxy/managers/jobs.py

@@ -1,6 +1,7 @@
 import json
 import logging
 import typing
+from datetime import datetime
 
 from boltons.iterutils import remap
 from pydantic import (
@@ -107,7 +108,7 @@ class JobManager:
 
         def build_and_apply_filters(query, objects, filter_func):
             if objects is not None:
-                if isinstance(objects, str):
+                if isinstance(objects, str) or isinstance(objects, datetime):
                     query = query.filter(filter_func(objects))
                 elif isinstance(objects, list):
                     t = []

lib/galaxy/model/security.py

@@ -500,7 +500,7 @@ class GalaxyRBACAgent(RBACAgent):
     def item_permission_map_for_add(self, trans, user_roles, libitems):
         return self.allow_action_on_libitems(trans, user_roles, self.permitted_actions.LIBRARY_ADD, libitems)
 
-    def can_access_dataset(self, user_roles, dataset):
+    def can_access_dataset(self, user_roles, dataset: galaxy.model.Dataset):
         # SM: dataset_is_public will access dataset.actions, which is a
         # backref that causes a query to be made to DatasetPermissions
         retval = self.dataset_is_public(dataset) or self.allow_action(
@@ -1122,7 +1122,7 @@ class GalaxyRBACAgent(RBACAgent):
             if not dataset.purged and not self.dataset_is_public(dataset):
                 self.make_dataset_public(dataset)
 
-    def dataset_is_public(self, dataset):
+    def dataset_is_public(self, dataset: galaxy.model.Dataset):
         """
         A dataset is considered public if there are no "access" actions
         associated with it.  Any other actions ( 'manage permissions',

lib/galaxy/objectstore/__init__.py

@@ -653,9 +653,11 @@ class DiskObjectStore(ConcreteObjectStore):
             if entire_dir and (extra_dir or obj_dir):
                 shutil.rmtree(path)
                 return True
-            if self._exists(obj, **kwargs):
-                os.remove(path)
-                return True
+            os.remove(path)
+            return True
+        except FileNotFoundError:
+            # Absolutely possible that a delete request races, but that's "fine".
+            return True
         except OSError as ex:
             log.critical(f"{self.__get_filename(obj, **kwargs)} delete error {ex}")
         return False

lib/galaxy/schema/schema.py

@@ -1112,8 +1112,8 @@ class JobIndexQueryPayload(Model):
     user_id: Optional[DecodedDatabaseIdField] = None
     tool_ids: Optional[List[str]] = None
     tool_ids_like: Optional[List[str]] = None
-    date_range_min: Optional[str] = None
-    date_range_max: Optional[str] = None
+    date_range_min: Optional[datetime] = None
+    date_range_max: Optional[datetime] = None
     history_id: Optional[DecodedDatabaseIdField] = None
     workflow_id: Optional[DecodedDatabaseIdField] = None
     invocation_id: Optional[DecodedDatabaseIdField] = None

lib/galaxy/tools/__init__.py

@@ -120,7 +120,10 @@ from galaxy.util.bunch import Bunch
 from galaxy.util.dictifiable import Dictifiable
 from galaxy.util.expressions import ExpressionContext
 from galaxy.util.form_builder import SelectField
-from galaxy.util.json import safe_loads
+from galaxy.util.json import (
+    safe_loads,
+    swap_inf_nan,
+)
 from galaxy.util.rules_dsl import RuleSet
 from galaxy.util.template import (
     fill_template,
@@ -2461,7 +2464,7 @@ class Tool(Dictifiable):
                 "enctype": self.enctype,
             }
         )
-        return tool_model
+        return swap_inf_nan(tool_model)
 
     def populate_model(self, request_context, inputs, state_inputs, group_inputs, other_values=None):
         """

lib/galaxy/util/json.py

@@ -9,6 +9,7 @@ from collections.abc import (
     Mapping,
     Sequence,
 )
+from decimal import Decimal
 
 from ..util import unicodify
 
@@ -22,7 +23,8 @@ from_json_string = json.loads
 
 def swap_inf_nan(val):
     """
-    This takes an arbitrary object and preps it for jsonifying safely, templating Inf/NaN.
+    This takes an arbitrary object and preps it for jsonifying safely, templating Inf/NaN and
+    casting Decimal instances as strings.
     """
     if isinstance(val, str):
         # basestring first, because it's a sequence and would otherwise get caught below.
@@ -40,6 +42,8 @@ def swap_inf_nan(val):
             return "__-Infinity__"
         else:
             return val
+    elif isinstance(val, Decimal):
+        return str(val)
     else:
         return val
 
@@ -63,12 +67,12 @@ def safe_dumps(obj, **kwargs):
     """
     This is a wrapper around dumps that encodes Infinity and NaN values.  It's a
     fairly rare case (which will be low in request volume).  Basically, we tell
-    json.dumps to blow up if it encounters Infinity/NaN, and we 'fix' it before
-    re-encoding.
+    json.dumps to blow up if it encounters Infinity/NaN, or Decimal values
+    and we 'fix' it before re-encoding.
     """
     try:
         dumped = json.dumps(obj, allow_nan=False, **kwargs)
-    except ValueError:
+    except (ValueError, TypeError):
         obj = swap_inf_nan(obj)
         dumped = json.dumps(obj, allow_nan=False, **kwargs)
     if kwargs.get("escape_closing_tags", True):

lib/galaxy/webapps/galaxy/api/jobs.py

@@ -5,6 +5,7 @@ API operations on a jobs.
 """
 
 import logging
+from datetime import datetime
 from typing import (
     Any,
     Dict,
@@ -98,13 +99,13 @@ ToolIdLikeQueryParam: Optional[str] = Query(
     description="Limit listing of jobs to those that match one of the included tool ID sql-like patterns. If none, all are returned",
 )
 
-DateRangeMinQueryParam: Optional[str] = Query(
+DateRangeMinQueryParam: Optional[datetime] = Query(
     default=None,
     title="Date Range Minimum",
     description="Limit listing of jobs to those that are updated after specified date (e.g. '2014-01-01')",
 )
 
-DateRangeMaxQueryParam: Optional[str] = Query(
+DateRangeMaxQueryParam: Optional[datetime] = Query(
     default=None,
     title="Date Range Maximum",
     description="Limit listing of jobs to those that are updated before specified date (e.g. '2014-01-01')",
@@ -186,8 +187,8 @@ class FastAPIJobs:
         view: JobIndexViewEnum = ViewQueryParam,
         tool_id: Optional[str] = ToolIdQueryParam,
         tool_id_like: Optional[str] = ToolIdLikeQueryParam,
-        date_range_min: Optional[str] = DateRangeMinQueryParam,
-        date_range_max: Optional[str] = DateRangeMaxQueryParam,
+        date_range_min: Optional[datetime] = DateRangeMinQueryParam,
+        date_range_max: Optional[datetime] = DateRangeMaxQueryParam,
         history_id: Optional[EncodedDatabaseIdField] = HistoryIdQueryParam,
         workflow_id: Optional[EncodedDatabaseIdField] = WorkflowIdQueryParam,
         invocation_id: Optional[EncodedDatabaseIdField] = InvocationIdQueryParam,

lib/galaxy/webapps/galaxy/controllers/dataset.py

@@ -10,7 +10,6 @@ from markupsafe import escape
 
 from galaxy import (
     datatypes,
-    model,
     util,
     web,
 )
@@ -88,16 +87,6 @@ class DatasetInterface(BaseUIController, UsesAnnotations, UsesItemRatings, UsesE
             roles, dataset_association.dataset
         )
 
-    @web.expose
-    def errors(self, trans, id):
-        hda = trans.sa_session.query(model.HistoryDatasetAssociation).get(self.decode_id(id))
-
-        if not hda or not self._can_access_dataset(trans, hda):
-            return trans.show_error_message(
-                "Either this dataset does not exist or you do not have permission to access it."
-            )
-        return trans.fill_template("dataset/errors.mako", hda=hda)
-
     @web.expose
     def stdout(self, trans, dataset_id=None, **kwargs):
         trans.response.set_content_type("text/plain")
@@ -713,6 +702,10 @@ class DatasetInterface(BaseUIController, UsesAnnotations, UsesItemRatings, UsesE
         **kwds,
     ):
         """Access to external display applications"""
+        if None in [app_name, link_name]:
+            return trans.show_error_message("A display application name and link name must be provided.")
+        app_name = unquote_plus(app_name)
+        link_name = unquote_plus(link_name)
         # Build list of parameters to pass in to display application logic (app_kwds)
         app_kwds = {}
         for name, value in dict(kwds).items():  # clone kwds because we remove stuff as we go.
@@ -734,10 +727,6 @@ class DatasetInterface(BaseUIController, UsesAnnotations, UsesItemRatings, UsesE
         else:
             user_roles = []
         # Decode application name and link name
-        app_name = unquote_plus(app_name)
-        link_name = unquote_plus(link_name)
-        if None in [app_name, link_name]:
-            return trans.show_error_message("A display application name and link name must be provided.")
         if self._can_access_dataset(trans, data, additional_roles=user_roles):
             msg = []
             preparable_steps = []

lib/galaxy/webapps/galaxy/controllers/root.py

@@ -106,8 +106,9 @@ class RootController(controller.JSAppLauncher, UsesAnnotations):
         if "authz_method" in kwd:
             authz_method = kwd["authz_method"]
         if data:
-            current_user_roles = trans.get_current_user_roles()
-            if authz_method == "rbac" and trans.app.security_agent.can_access_dataset(current_user_roles, data):
+            if authz_method == "rbac" and trans.app.security_agent.can_access_dataset(
+                trans.get_current_user_roles(), data.dataset
+            ):
                 trans.response.set_content_type(data.get_mime())
                 trans.log_event(f"Formatted dataset id {str(id)} for display at {display_app}")
                 return data.as_display_type(display_app, **kwd)

lib/galaxy_test/api/test_jobs.py

@@ -82,14 +82,14 @@ class JobsApiTestCase(ApiTestCase, TestsTools):
 
     @uses_test_history(require_new=True)
     def test_index_date_filter(self, history_id):
-        self.__history_with_new_dataset(history_id)
         two_weeks_ago = (datetime.datetime.utcnow() - datetime.timedelta(14)).isoformat()
         last_week = (datetime.datetime.utcnow() - datetime.timedelta(7)).isoformat()
         next_week = (datetime.datetime.utcnow() + datetime.timedelta(7)).isoformat()
         today = datetime.datetime.utcnow().isoformat()
         tomorrow = (datetime.datetime.utcnow() + datetime.timedelta(1)).isoformat()
+        self.__history_with_new_dataset(history_id)
 
-        jobs = self.__jobs_index(data={"date_range_min": today[0:10], "date_range_max": tomorrow[0:10]})
+        jobs = self.__jobs_index(data={"date_range_min": today, "date_range_max": tomorrow})
         assert len(jobs) > 0
         today_job_id = jobs[0]["id"]
 

test/unit/util/test_json.py

@@ -0,0 +1,25 @@
+from decimal import Decimal
+
+import pytest
+
+from galaxy.util.json import (
+    safe_dumps,
+    swap_inf_nan,
+)
+
+
+@pytest.mark.parametrize(
+    "val,expected_val",
+    [
+        (float("inf"), "__Infinity__"),
+        (float("-inf"), "__-Infinity__"),
+        (float("NaN"), "__NaN__"),
+        (Decimal("1"), "1"),
+    ],
+)
+def test_swap_inf_nan(val, expected_val):
+    assert swap_inf_nan(val) == expected_val
+
+
+def test_safe_dumps():
+    assert safe_dumps({"a": Decimal("0.1")}) == """{"a": "0.1"}"""